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It is not uncommon to observe some EEA1 in "spots" in the nuclei (I see it quite often). However, as far as I could see in the image, the majority of the EEA1 is there rather than in the cytoplasm - THAT is not normal.

My protocol is a bit different, for fixation I use 4% PFA (20 min, RT) and for permeabilization 0,5% Tween-20 in PBS (20 min, 37°C). Washing 3 times with PBS confocal microscopy between each step is required. Usually, I don't use any type of shaking when staining cells, but that's not important in this case.

I gather that you use direct IF, so specificity should not be a problem. If not - check cross-reactivity. Also, when incubating too long with secondary antibody, the non-specific staining is more likely to happen.

What are the cells in question? Are they usually adherent or did you use cytospin to adhere them? Some manipulations with the cells before the staining process can cause them to change their subcellular structures and their position.

Did you use confocal microscope to take that image? If not, you may have observed the EEA1 that is in cytoplasm ABOVE the cell nucleus.